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How can I delete the custom colors?

In the current presentation, so that other people editing the same presentation have the custom colors available.

On your computer, so that you have the custom colors available in other (e.g., new) presentations.

There is currently no official means to clear the custom colors list.
While there is no way at all to remove custom colors from a presentation file, the part of the list that is stored on your computer (the part below the divider line) can in fact be cleared.
However, be aware that you will lose some other settings, too, including your custom precisions list and possibly your license key (which you can re-enter on the next start of PowerPoint or Excel).

The custom-defined colors are stored in a file and get cleared when you remove the file.
The following steps describe how to do this:

Open a new Windows Explorer window.

Type %APPDATA%\think-cell into the address field and press Enter.

Note: This step might delete the license key from your system.
Please ensure that you have a valid license at hand before you proceed.